After some email discussions with Eric Woodruff, I have decided to post here to help others who might want to also remove the "Send comments on this topic to [email address]" line in the footer of a help file.
1) Open your .shfbproj in Sandcastle HFB
2) In its Project Explorer, right-click on your Project file and select Add -> New Item -> Resource Item File
3) Double click on the file it added (default name is Resource Item File.items)
4) Locate the "comments" items and delete it's contents. (You could also replace with your own custom code)
5) save and build your project
You should notice that the line "Send comments...." is now missing from the footer of each page.
Again, Thanks Eric for helping me out on this.